8ID8: TUG891 bound GPR120-Gi complex

Cryo-EM structure of the TUG891 bound GPR120-Gi complex. Determined by electron microscopy at 3.0 Å resolution. Released 15 Mar 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,635
Mol. weight: 156.82 kDa
Ligands: YN9
Released: 15 Mar 2023

Explore 8ID8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ID8 contains 30 α-helices and 67 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	1
α-helix	46-52	7
β-strand	185-191	7	1
β-strand	194-200	7	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-350	20

Chain B: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	3-24	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	49-51	3	3
β-strand	58-63	6	4
β-strand	70-74	5	4
β-strand	78-82	5	4
β-strand	89-94	6	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	157-161	5	6
β-strand	166-168	3	6
β-strand	178-180	3	6
β-strand	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	217-223	7	7
β-strand	229-232	4	8
β-strand	240	1	8
β-strand	243-245	3	8
β-strand	250-254	5	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
α-helix	38-67	30
α-helix	69-72	4
α-helix	79-100	22
α-helix	108-141	34
α-helix	153-175	23
β-strand	177-181	5	10
β-strand	192-196	5	10
α-helix	204-212	9
α-helix	213-217	5
α-helix	218-241	24
α-helix	252-276	25
α-helix	278-293	16
α-helix	305-320	16

Chain S: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	12	1	12
β-strand	17-24	8	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	68-73	6	11
β-strand	78-84	7	11
β-strand	92-94	3	14
β-strand	95-99	5	13
β-strand	111	1	13
β-strand	115-117	3	14
β-strand	119	1	12
β-strand	141-143	3	15
β-strand	147	1	16
β-strand	156-162	7	15
β-strand	167	1	17
β-strand	173	1	17
β-strand	175-179	5	18
β-strand	180	1	16
β-strand	187-191	5	18
β-strand	195-196	2	18
β-strand	204-209	6	15
β-strand	212-217	6	15
β-strand	227-228	2	16
β-strand	230-232	3	18
α-helix	238	1
β-strand	240	1	18
β-strand	244-245	2	16

Chain Y: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	339	Homo sapiens	P62873 (AlphaFold model)
Free fatty acid receptor 4	R	protein	361	Homo sapiens	Q5NUL3 (AlphaFold model)
scFv16	S	protein	285	Homo sapiens
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	Y	protein	71	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8ID8_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>8ID8_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
SELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAM
HWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNIC
SIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFT
GHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAF
ATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALK
ADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (R), FASTA

>8ID8_3 Free fatty acid receptor 4 (chains R)
MSPECARAAGDAPLRSLEQANRTRFPFFSDVKGDHRLVLAAVETTVLVLIFAVSLLGNVC
ALVLVARRRRRGATACLVLNLFCADLLFISAIPLVLAVRWTEAWLLGPVACHLLFYVMTL
SGSVTILTLAAVSLERMVCIVHLQRGVRGPGRRARAVLLALIWGYSAVAALPLCVFFRVV
PQRLPGADQEISICTLIWPTIPGEISWDVSFVTLNFLVPGLVIVISYSKILQITKASRKR
LTVSLAYSESHQIRVSQQDFRLFRTLFLLMVSFFIMWSPIIITILLILIQNFKQDLVIWP
SLFFWVVAFTFANSALNPILYNMTLCRNEWKKIFCCFWFPEKGAILTDTSVKRNDLSIIS
G

Sequence of entity 4 (S), FASTA

>8ID8_4 scFv16 (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Sequence of entity 5 (Y), FASTA

>8ID8_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains Y)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Ligands and cofactors

ID	Name	Formula	Copies
YN9	3-{4-[(4-fluoro-4'-methyl[1,1'-biphenyl]-2-yl)methoxy]phenyl}propanoic acid	C23 H21 F O3	1

Primary citation

Unsaturated bond recognition leads to biased signal in a fatty acid receptor. Mao, C., Xiao, P., Tao, X.N. et al. Science (2023) 380:eadd6220-eadd6220. DOI 10.1126/science.add6220 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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